Junk DNA: Scientific American Gets It Wrong (again)

In 1972 the late geneticist Susumu Ohno coined the term "junk DNA" to describe all noncoding sections of a genome, most of which consist of repeated segments scattered randomly throughout the genome.

This is very misleading. First, nobody today would argue that all noncoding DNA is junk and I very much doubt that Ohno made that argument in 1972 (the orignal paper is hard to get). We know tons of examples of noncoding DNA that isn't junk.

Second, the focus on repetitive DNA is inappropriate. Lots of junk DNA is non-repetitive; pseudogenes are a prime example. Makalowski has a particular bee in his bonnet over repetitive DNA but that shouldn't be allowed to warp his judgement when responding to a question in Scientific American.

Although very catchy, the term "junk DNA" repelled mainstream researchers from studying noncoding genetic material for many years. After all, who would like to dig through genomic garbage?

Nonsense. Researchers have been exploring noncoding DNA intensely for the past 40 years. That's why we know so much about regulatory sequences. Regulatory sequences are noncoding DNA that control gene expression.

Furthermore, even when it comes to true junk DNA, properly defined, hundreds of papers have been published. Lots of us have been very interested in junk DNA—at least in part in order to find out whether it has a function. This work led to the indentification of hundreds of pseudogenes, the unimportance of most intron sequences, and the degeneracy of LINES and SINES. There's lots more. I don't know of any researchers that were "repelled" from studying junk DNA. Many took it as a challenge.

Thankfully, though, there are some clochards who, at the risk of being ridiculed, explore unpopular territories. And it is because of them that in the early 1990s, the view of junk DNA, especially repetitive elements, began to change. In fact, more and more biologists now regard repetitive elements as genomic treasures. It appears that these transposable elements are not useless DNA. Instead, they interact with the surrounding genomic environment and increase the ability of the organism to evolve by serving as hot spots for genetic recombination and by providing new and important signals for regulating gene expression.

Serving as hotspots for genetic recombination is not a "function" of most junk DNA. Furthermore, it's not at all clear that increasing recombination at a particular site will have any effect on future survival. Finally, signals for regulating gene expression have been known for decades. These signals are not junk DNA.

Genomes are dynamic entities: new functional elements appear and old ones become extinct. And so, junk DNA can evolve into functional DNA. The late evolutionary biologist Stephen Jay Gould and paleontologist Elisabeth Vrba, now at Yale University, employed the term "exaptation" to explain how different genomic entities may take on new roles regardless of their original function—even if they originally served no purpose at all. With the wealth of genomic sequence information at our disposal, we are slowly uncovering the importance of non-protein-coding DNA.

The occasional piece of junk DNA may be co-opted to become part of a newly evolved function. This does not mean that all junk DNA has a function. That's a classic error in logic more common in freshmen undegraduates than in "expert" Professors.

... These and countless other examples demonstrate that repetitive elements are hardly "junk" but rather are important, integral components of eukaryotic genomes. Risking the personification of biological processes, we can say that evolution is too wise to waste this valuable information.

From time to time we will find examples of some little bit of junk DNA that acquires a function. This does not mean that all junk DNA has a function. And it certainly doesn't mean that all DNA has now been shown to be "important, integral components of eukaryotic genomes." Most of our DNA is still junk. It turns out that evolution really isn't so smart after all.

13 comments:

I find today's SciAm quite depressing, because I remember the infinitely superior magazine published under that name when I was young, which inspired so many budding scientists and published so many articles, by leading scientists, of sufficient quality and seriousness to be useful reading for lower-division college courses. It's just one small instance of the incessant dumbing-down of everything.

I agree. The decline of Scientific American is more sad because it has fallen so far. I used to read it when I was a teenager in the 60's. At that time you could read articles by the leading lights in science.

Now that the second-stringers, and the taxi squad have taken over it's no longer worth reading. I'll keep my subscription just so I can take potshots once in a while.

But the thing is that Scientific American was meant to be written for the general public and not those who know a lot about these things, for the most part. Is it not accurate to say that according to the general public's view of "Junk DNA" that this may be what was wired into the general public in the first place?

I personally think that this is more a problem of communications of those in between more than anything else.

Agree on the decline and fall of SciAm. I read it occasionally during the 70s, then subscribed around 1982. It was hard to read -- detailed descriptions of experiments designed to tease out some fact of bio, psych or physics; stuff like that. I often had to work to understand the articles. This was a Good Thing: we enjoyed every issue, and learned a lot about all kinds of fields.

Then sometime in the late 90s the rot set in: more "Science Nooz" fluff, mucking with fonts and formats in search of...I dunno, but it wasn't readability, anyway. SciAm became little different from Discover (which itself was moving down-market). After 20 years we ditched our sub.

Yes the joy is gone in the past nineties issues, but the old magazines eighties and early nineties I have from the eighties are still delightful to read and study. I think the strong point of sciam was not having any general theme but interesting research in any field. I agree it gives you a feel for all kinds of fields involved in a subject. I am mostly in fisheries, fish culture and ecology, but of course mathematics, physics, chemistry, climate, history all touch on such a subject. It was maybe hard to read but less so then articles from Nature or Science that are more like work and require more effort and more in depth a priori knowledge of the field. Maybe it was the great graphics of sciam that made it special.

I agree with all that SciAm, in general, is "not as it used to be", and that its record of handling the "junk" DNA is in particularly unfortunate (see featuring the coverage in http://www.junkdna.com - lead story)

On the positive side, Kenny is quite right that there is a huge "communication challenge" regarding what used to be "junk" DNA (before PostGenetics Society formally abandoned the notion; http://www.postgenetics.org).

Part of handling this challenge, which will most likely *not* be tackled by SciAm (or any news media) is the realization that we already left the "junk" notion and in PostGenetics (in the PostModern era of Genomics "beyond Genes") there are specific issues to address, with an agenda that should be easily understood for all:

"Most, if not all hereditary diseases have their origin not in the 'genes' - but in the 98.7% of the human DNA".

There is practically nobody who himself/herself, or somebody in the family and friends does not have such "non-coding DNA disease" patients. Diseases can be as "harmless" as "male pattern baldness" - but often as dreadful as Parkinson's or Alzheimer's, skizophrenia, diabetes or bipolar syndrome.

In my opinion, Society (such as International PostGenetics Society) and society (such as tax-payers) need to raise awareness that apart from some devoted "clochards" (truly, pioneers) there is a serious neglect of this issue.

First, nobody today would argue that all noncoding DNA is junk and I very much doubt that Ohno made that argument in 1972 (the orignal paper is hard to get).

he considers promoter and operator regions to be parts of genes "genes", and thus not junk.

the argument is that there is some sort of advantage to having intranscribable or untranslatable pieces of DNA between genes for a number of regions. He proposes that these regions are "the remains of nature's experiments which failed", i.e. pseudogenes. following this analogy, the genome is somethink like a junkyard.

it's worth noting he never used the phrase "junk DNA", it just caught on because of his title (So much "junk" in our genome").

What is striking to me is that someone who sees himself a scientist at University of Toronto makes comments without having seen Ohno's original paper. [ By the way, p-ter, the paper is called 'So much "junk" DNA in our genome', so your position regarding the use of junk DNA does not stand. ] It is hard for me to believe that UofT does not have some sort of inter-library loan system, and the paper could have been asked for through those channels. Or, you can even find excerpts from it online, such as here: http://www.junkdna.com/ohno.html, but of course, you need to search for it.

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The old argument of design in nature, as given by Paley, which formerlyseemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.

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Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.

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My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

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Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

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TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

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Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.